Missing Files After Opening Project

I am using a custom Source of UE 4.25.1, last night I saved my project closed UE4 and turned my computer off. Everything closed normally.

Today I turned on my computer and opened UE4, and it said Loading Assets (something like that) of around 8,000 files.
All of my Editor settings have been returned to default and I have missing Files.

Also source control has been disconnected.

The missing files are missing in File Explorer as well. So I am now missing random assets from my project and missing my map I have spent days on. So today I am going to be reconnecting source control and trying to salvage this I suppose.

Can anyone help me figure out WHY this happened, so I can avoid it in the future.

This happened to me too. I really have no idea what happened. Did you ever figure out what happened?